Hmm. I think I always got from the books that LMB was pretty aware of how imperialistic Barrayar's behavior toward Komarr was. There is sort of the complicating factor of the wormhole, and the fact that Komarr proved themselves, ahem, a bit untrustworthy. So there's the sense in the books that Barrayar somehow didn't have a choice but to conquer Komarr, which is perhaps the most problematic aspect of things from my POV.

I think what I generally took from the books is that the characters are all good people, but the systems of which they are a part are often deeply messed up. Empires always are (and democracies are often not much better - Beta has its own issues). Cordelia is a great POV character for this reason - even after several decades on Barrayar, she isn't really "inside" the system the way that Miles and Ivan and Gregor (and Aral) are. She can see the ways in which it is a truly terrible place for many people, even while loving people who love Barrayar.

In fewer words: I think LMB is pretty aware of the world she's created.